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Caracterización genética de aislamientos de Phytophthora infestans en las
zonas productoras de papa de los departamentos de Antioquia, Boyacá,
Cundinamarca y Norte de Santander (Co...
Article  in  Actualidades Biológicas · February 2010
DOI: 10.17533/udea.acbi.4725
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FACULTAD DE AGRONOMÍA
CONTENIDO
Apartado Aéreo 14490, Bogotá-Colombia
Teléfonos: (571) 316 5498 / 316 5000 ext. 19043 y 19088
Telefax: 3165176. agrocol_fabog@unal.edu.co
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VOLUMEN XXVIII, No. 3 sEptIEMBRE-dICIEMBRE 2010 IssN 0120-9965
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FACULTAD DE AGRONOMÍA
131 EDITORIAL
fITOmEjOramIENTO, rECursOs gENéTICOs y bIOlOgía mOlECular
363 Análisis de la interacción soya-cepa (Bradyrhizobium japonicum) x ambiente, en oxisoles de 
la Orinoquia colombiana
Analyses of soybean-stain (Bradyrhizobium japonicum) x environment interaction, in oxisols of the 
colombian Orinoquia
Rubén A. Valencia R. y Gustavo Ligarreto M.
375 Artificial microRNAs and their applications in plant molecular biology
MicroARNs artificiales y sus aplicaciones en biología molecular de plantas
Álvaro Luis Pérez-Quintero and Camilo López
PrOTECCIÓN DE CulTIVOs
385 Population structure of Phytophthora infestans in potato crops from Antioquia, Boyaca, 
Cundinamarca, and Norte de Santander (Colombia)
Estructura poblacional de Phytophthora infestans en cultivos de papa de Antioquia, Boyacá, 
Cundinamarca y Norte de Santander (Colombia)
Bernardo Silva A., José Miguel Cotes, and Mauricio Marín M.
393 Molecular identification and characterization of Colletotrichum sp. isolates from tahiti lime, 
tamarillo, and mango
Identificación y caracterización molecular de Colletotrichum sp. aislados de lima tahití, tomate 
de árbol y mango
Adriana Sanabria, George Mahuku, Segenet Kelemu, Marcela Cadavid, Celsa García, Juan C. Hío, Érika 
Martínez, and Jairo A. Osorio
403 Determination of levels of damage caused by different densities of Tuta absoluta populations 
(Lepidoptera: Gelechiidae) under greenhouse conditions
Determinación de niveles de daño ocasionados por diferentes densidades de población de Tuta 
absoluta (Lepidoptera: Gelechiidae) en tomate bajo invernadero
Liliana Cely P., Fernando Cantor, and Daniel Rodríguez
suElOs, fErTIlIZaCIÓN y maNEjO DE aguas
415 14C-glyphosate mineralization and follow up of the dynamics of Pseudomonas sp. 
populations in three soils under different uses in Tolima (Colombia)
Mineralización de 14C-glifosato y seguimiento de la dinámica de las poblaciones de Pseudomonas 
sp. en tres suelos del departamento del Tolima (Colombia) sometidos a diferente uso
Liliana Figueroa del Castillo, Myriam Rocío Melgarejo P., Cilia L. Fuentes de Piedrahíta, and Amanda 
Lozano de Yunda
423 Effect of conventional and organic vegetable production systems on soil chemical 
properties in the Bogota plateau (Colombia)
Efecto de los sistemas de producción convencional y orgánico de hortalizas en las propiedades 
químicas del suelo en la Sabana de Bogotá (Colombia)
Andrés Fernando Forero, and Hugo Escobar
ECONOmía y DEsarrOllO rural
431 Keys for rural territorial development
Claves del desarrollo territorial rural
Juan Patricio Molina
439 Lessons on rural development, challenges and approaches
Lecciones del desarrollo rural, desafíos y enfoques
Absalón Machado
447 Elementospara una renovación de las estrategias de desarrollo rural
Elements for Rural Development Strategies Renewal
Alexander Schejtman
457 Identification and systems methodologies for territorial delimitation1
Identificación y metodologías de sistemas para la delimitación de territorios
Iván Montoya R. and Alexandra Montoya R.
469 Territorial perspective of agricultural extension policies in Colombia
Perspectiva territorial de las políticas de asistencia técnica agropecuaria en Colombia
Juan Patricio Molina
477 Rural development in the European Union: the concept and the policy
El desarrollo rural en la Unión Europea: el concepto y la política
Rosa Gallardo-Cobos
485 Emprendimientos y empresas agrarias y rurales más sustentables, para la sustentabilidad 
de los territorios
Agrarians and rural ventures and companies more sustainable, for the sustainability of the 
territories
Adriana Chaparro-Africano
493 Manejo de stakeholders como estrategia para la administración de proyectos de desarrollo 
en territorios rurales
Stakeholders management as a strategy for the administration of development projects in rural 
territories
Jorge Enrique Ángel P.
503 From the associative companies to the nuclei of rural entrepreneurs
De las empresas asociativas a los núcleos de emprendedores rurales
Álvaro Parrado
509 El valor estratégico del turismo rural como alternativa sostenible de desarrollo territorial 
rural
The strategic value of rural tourism as a sustainable alternative for a territorial rural development
Samuel Pérez
519 El desarrollo rural de Medellín Una perspectiva desde el desarrollo endógeno
The rural development of Medellin A perspective from endogenous development
Laura Moisá y Adolfo Hernández
529 Desarrollo de la metodología Innovación Rural Participativa en la Zona Andina Central de 
Colombia
Development of methodology Participatory Rural Innovation in the Central Andean region of 
Colombia
Omar Gutiérrez
539 Las industrias sensibles de Nariño
The sensitive industries of Nariño
Ilich Ruiz- Reynel
549 Rural development between farmers and policy executors: case for the Tequedama Province 
(Cundinamarca-Colombia)
Desarrollo rural entre campesinos y ejecutores de políticas: caso provincia del Tequendama 
(Cundinamarca-Colombia)
Fabio Alberto Pachón-Ariza, and María Nelly Argüello-Blanco
559 Socio-political effects of the Urrá I hydroelectric construction in the Embera Katio 
Indigenous community
Efectos sociopolíticos de la construcción de la hidroeléctrica Urrá I en la comunidad indígena 
Embera Katio
Madelaide Morales-Ruiz, and Fabio Alberto Pachón-Ariza
567 The municipal territorial management and multi-functionality: Analysis of a bilateral 
international project in Copan (Honduras)
La gestión municipal territorial y la multifuncionalidad: análisis de un proyecto de cooperación 
bilateral en Copán (Honduras)
Álvaro Rivas and Pablo Enrique Avendaño
575 Updating peasant competencies to mitigate poverty in the Chorti community, Copan 
(Honduras)
Actualización de competencias para mitigar la pobreza en campesinos de la comunidad 
Chortí de Copán (Honduras)
Álvaro Rivas, Pablo Enrique Avendaño, and Heimar Quintero
585 Nematodos asociados con cultivos de arroz en Huila y Tolima
Nematode associated with rice crops in Huila and Tolima
Lilliana M. Hoyos-Carvajal y Javier G. Moya
aNExOs
595 Requisitos para publicar en la Revista Agronomía Colombiana
Agronomía Colombiana es una publicación técnico-científica clasificada por Colciencias en la categoría A2 
del Índice Nacional de Publicaciones Seriadas y Científicas y Tecnológicas (Publindex) (Colombia), además 
está indexada en Scientific Electronic Library Online (SciELO). A nivel internacional la revista se halla 
referenciada en Latindex, AGRIS (FAO) e integrada en CABI Full Text y en las siguientes bases de datos de 
CAB-ABSTRACTS: Agricultural Engineering Abstracts, Agroforestry Abstracts, Crop Physiology Abstracts, 
Field Crop Abstracts, Grasslands and Forage Abstracts, Horticultural Science Abstracts, Irrigation and 
Drainage Abstracts, Maize Abstracts, Nematological Abstracts, Ornamental Horticulture, Plant Breeding 
Abstracts, Plant Growth Regulator Abstracts, Postharvest News and Information, Potato Abstracts, Review 
of Agricultural Entomology, Review of Aromatic and Medicinal Plants, Review of Plant Pathology, Rice Abs-
tracts, Seed Abstracts, Soils and Fertilizers, Sugar Industry Abstracts, Weed Abstracts y World Agricultural 
Economics and Rural Sociology Abstracts.
COMITé EDITORIAL
Juan Pablo Fernández Trujillo, Departamento de Ingeniería de Alimentos y del 
Equipamiento Agrícola, Universidad Politécnica de Cartagena, Murcia, 
España.
Miguel Jordan, Escuela de Biotecnología, Universidad Mayor, Santiago, Chile.
Gustavo Ligarreto, Facultad de Agronomía, Universidad Nacional de Colombia, 
Bogotá.
Stanislav Magnitskiy, Facultad de Agronomía, Universidad Nacional de 
Colombia, Bogotá.
Luis J. Martínez, Facultad de Agronomía, Universidad Nacional de Colombia, 
Bogotá.
Iván Montoya, Facultad de Agronomía, Universidad Nacional de Colombia, 
Bogotá.
Guido Plaza, Facultad de Agronomía, Universidad Nacional de Colombia, 
Bogotá.
Jürgen Pohlan, Institut für Tropische Landwirtschaft Leipzig e. V., Alemania.
Paulo César Tavares de Melo, Escola Superior de Agricultura Luiz de Queiroz, 
Universidade de São Paulo, Piracicaba, SP, Brasil.
Christian Ulrichs, Division Plant Ecophysiology, Faculty of Agriculture and 
Horticulture, Humboldt-Universität zu Berlin, Alemania.
COMITé CIENTÍFICO
Agim Ballvora, Max Planck Institute for Plant Breeding Research, Köln, 
Alemania.
Yoav Bashan, Microbiología Ambiental, Centro de Investigaciones Biológicas 
del Noroeste (CIBNOR), La Paz, México.
Carmen Büttner, Division Phytomedicine, Faculty of Agriculture and 
Horticulture, Humboldt-Universität zu Berlin, Alemania.
Daniel G. Debouck, Genetic Resources Unit, Centro Internacional de 
Agricultura Tropical (CIAT), Cali, Colombia.
Derly J. Henriques da Silva, Departamento de Fitotecnia, Universidade Federal 
de Viçosa, Viçosa, MG, Brasil.
Antonio A. Monteiro, Instituto Superior de Agronomía, Universidad Técnica de 
Lisboa, Portugal.
Idupulapati Rao, Tropical Soil Biology and Fertility Institute, Centro 
Internacional de Agricultura Tropical (CIAT), Cali, Colombia.
Manuel Talón, Instituto Valenciano de Investigaciones Agrarias (IVIA), 
Moncada, Valencia, España.
Lorenzo Zacarías, Instituto de Agroquímica y Tecnología de Alimentos (IATA-
CSIC), Burjassot, Valencia, España.
 
SEPTIEMBRE-DICIEMBRE 2010VOLUMEN XXVIII No. 3 ISSN 0120-9965
PublICaCIÓN DE CaraCTEr CIENTífICO-TéCNICO DE la faCulTaD DE agrONOmía DE la uNIVErsIDaD NaCIONal DE COlOmbIa, bOgOTá
©2010 Agronomía Colombiana 
Universidad Nacional de Colombia
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RECTOR
MoISéS wASSeRMAn
DECANO
MARIA ISABeL CHACón
DIRECTOR-EDITOR
GUSTAvo LIGARReTo
Tarifa Postal Reducida No. 2010-404. 4-72 La Red Postal de Colombia, vence 31 de Dic. 2010
nuestra portada
El enfoque territorial pilar del desarrollo rural. 
Fotos: Omar Gutiérrez y Jorge Ángel, 2010.
Recceived for publication: 5 March, 2010. Accepted for publication: 13 December, 2010.
1 Laboratory of Cellular and Molecular Biology, Faculty of Science, Universidad Nacional de Colombia, Medellín (Colombia).
2 Department of Science Agronomy, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Medellín (Colombia).
3 Corresponding author. mamarinm@unal.edu.co
Agronomía Colombiana 28(3), 385-392, 2010
In Colombia, potato blight is limiting in potato crops be-
cause of favorable climatic conditions for its development 
and the cultivation of materials highly susceptible to the 
pathogen populations (Jaramillo, 2004). Management of 
this disease has been primarily based on the rotation of 
fungicides with protective and systemic action (Erwin and 
Ribeiro, 1996). Nevertheless, the effectiveness of some of 
these products has been gradually reduced as a result of the 
onset of resistance in the pathogen populations, given the 
PROTECCIÓN DE CULTIVOS
Population structure of Phytophthora infestans in potato crops from 
Antioquia, Boyaca, Cundinamarca, and Norte de Santander (Colombia)
Estructura poblacional de Phytophthora infestans en cultivos de papa de 
Antioquia, Boyacá, Cundinamarca y Norte de Santander (Colombia)
Bernardo Silva A.1, José Miguel Cotes2, and Mauricio Marín M.1, 3
Introduction
One of the most limiting diseases in potato crops (Solanum 
tuberosum and S. phureja) is the potato blight or late blight, 
caused by the oomycete Phytophthora infestans (Garelik, 
2002). P. infestans is considered a serious threat for the 
planet’s food safety, to the point that its detrimental effect 
on world agriculture has been estimated close to 5-billion 
US Dollars per year (Duncan, 1999; Kamoun, 2003). 
ABSTRACT RESUMEN
Potato late blight (Phytophthora infestans), is this crop’s most 
important disease in Colombia. An alternative in reducing 
the high dependence on fungicides to control the potato late 
blight includes developing resistant plant varieties, such as the 
ones recently delivered in Colombia (Pastusa Suprema and Es-
meralda), which show high acceptance levels among growers. 
However, maintenance of resistance in these materials, as well 
as the effectiveness of systemic fungicides used to control this 
disease depends on management practices and evolutionary 
dynamics of P. infestans in each of the potato-growing regions. 
This research evaluated such a condition through a population 
structure study of isolates obtained from the departments of 
Antioquia, Boyaca, Cundinamarca, and Norte de Santander, 
using AFLP (Amplified Fragment Length Polymorphism) mo-
lecular markers. Results indicated the occurrence of low levels 
of genetic variability within each of the four populations and an 
important population differentiation among them, especially 
regarding the population of P. infestans from Antioquia against 
the middle-east populations. This suggests that besides the 
tests usually made in Cundinamarca and Boyaca to evaluate 
resistant materials for P. infestans, different tests in Antioquia 
should also be included.
La gota de la papa (Phytophthora infestans) es la enfermedad 
más limitante del cultivo en Colombia. Una alternativa para 
reducir la dependencia de los fungicidas para el control de la 
gota, incluye la generación de variedades con resistencia al 
patógeno, algunas de las cuales (Pastusa Suprema y Esmer-
alda) se han entregado a los agricultores con buenos niveles 
de aceptación. Sin embargo, tanto el mantenimiento de los 
niveles de resistencia de estos materiales como la efectividad de 
los fungicidas que se utilizan para su control, dependen de las 
prácticas de manejo y de la dinámica evolutiva de P. infestans 
en cada región cultivadora. Este trabajo evaluó dicha dinámica 
a partir del estudio de la estructura poblacional del patógeno 
en los departamentos de Antioquia, Boyacá, Cundinamarca y 
Norte de Santander, mediante el empleo de marcadores AFLP 
(Amplified Fragment Length Polymorphism). Los resultados 
indicaron la ocurrencia de bajos niveles de variación al interior 
de las cuatro poblaciones, con una evidente diferenciación entre 
la población del patógeno de Antioquia con respecto a las de 
la región centro-oriente del país. Esto indica que la evaluación 
de variedades mejoradas de papa con resistencia a gota debe 
realizarse tanto en la sabana Cundiboyacense, como en las 
regiones cultivadoras de Antioquia.
Key words: AFLP, genetic variability, molecular markers, potato 
late blight.
Palabras clave: AFLP, variabilidad genética, marcadores mo-
leculares, gota de la papa.
386 Agron. Colomb. 28(3) 2010
pressure for selection exerted by current agricultural sys-
tems (Gisi and Cohen, 1996; Riveros et al., 2003). Different 
studies have shown that presence of specific mutations in 
genes codifying for target proteins of the fungicide action 
and of certain nucleotide sequences located in said gene 
promoters, are associated to the occurrence of specific 
mutations resistant to chemical molecules and that the 
onset sequence of these genetic changes is directly associ-
ated to the recombination rate in the sexual and parasexual 
cycles presented by fungi and oomycetes, as well as by the 
genetic structure of populations (Milgroom and Peever, 
2003; Damicone, 2004). 
A viable alternative to reduce the limitation imposed by 
the potato blight in the national potato production cor-
responds to the generation of improved varieties resistant 
against the pathogen, of which there are success cases like 
the “Monserrate” variety and the more recent market in-
troductions: “Pastusa Suprema” and “Esmeralda” (Santos 
et al., 2010). Nevertheless, maintenance of resistance levels 
of these materials and of others generated in the future will 
depend on the P. infestans population dynamics.
Traditionally, the populations of P. infestans have been 
characterized based on different phenotypic and genotypic 
markers, especially the electrophoretic pattern generated 
with the RG57 probe in RFLPs (restriction fragment length 
polymorphism), analysis of Gpi and Pep isoenzymes, level 
of sensitivity to metalaxyl fungicide, presence of virulent 
genes determined from differential hosts with R genes, mat-
ing type, and evaluation of the mitochondrial haplotypes 
(Fry et al., 1991; Goodwin et al., 1994; Griffith and Shaw, 
1998; Grunwald and Flier, 2005). Using these method-
ologies has led to determining that the populations of P. 
infestans are sub-structured from clonal lineages. 
Recent studies in Colombia have determined that the popu-
lation of P. infestans predominant in potato crops presents 
the IIa mitochondrial haplotype and the A1 mating type, 
which is associated to the EC-1 clonal lineage (Raigosa et 
al., 2009; Gilchrist et al., 2009; Silva et al., 2009). Recently, 
Vargas et al. (2009) conducted a characterization study of 
isolations of P. infestans from different solanaceae in the 
department of Cundinamarca and to a lesser extent in 
Antioquia, finding isolation with the A2 mating type from 
Physalis peruviana plants, besides a very low variation level 
in the population analyzed. In spite of the predominantly 
clonal condition of the P. infestans populations determined 
via phenotypic and genotypic evaluations previously 
described, studies using neutral molecular markers like 
RAPDs (Random Amplification of Polymorphic DNA) 
and AFLPs, have revealed the existence of an appreciabledegree of genetic variability within the lineages of the 
oomycete (Mahuku et al., 2000; Páez et al., 2004). A spe-
cially interesting work was done by Abu-El Samen et al. 
(2003), whose RAPD and AFLP electrophoretic patterns 
(80 RAPD primers and 18 pairs of AFLP primers) from 32 
monozoosporic isolates, asexually derived from a parental 
isolation, presented a high degree of variation, for which 
the authors suggest that events of mitotic recombination, 
parasexuality, and spontaneous mutations, play a fun-
damental role in generating new P. infestans genotypes. 
Also, studies by Mesa et al. (2008) and Raigosa et al. (2009) 
using molecular markers in P. infestans populations from 
different hosts in Colombia have determined the existence 
of variation levels within the clades representing oomycete 
genetic lineages reported in the country.
The basis for design of new strategies of chemical or genetic 
control of potato blight in the country must be founded 
on studies defining the characteristics of the P. infestans 
populations in the different potato growing regions. This 
situation constituted the central objective for this research, 
when studying the P. infestans populations from the depart-
ments of Antioquia, Boyacá, Cundinamarca, and Norte de 
Santander by using AFLP molecular markers.
Materials and methods
Isolations 
We gathered symptomatic samples from plants from differ-
ent kinds of potato varieties from S. tuberosum ssp. andi-
gena and S. phureja, in the main grower municipalities in 
the departments of Antioquia, Boyaca, and Cundinamarca. 
Additionally, DNA was included of isolates previously 
collected and stored in the Laboratory of Cellular and 
Molecular Biology at Universidad Nacional de Colombia 
in Medellin, from the three departments mentioned and 
Norte de Santander. 
Thus, a total of 40 isolates were analyzed from each of the 
departments for a total of 160 isolates. From these isolates, 
71 were collected from S. tuberosum “Parda Pastusa” vari-
ety, 24 from S. tuberosum “Diacol Capiro” variety, 17 from 
S. phureja “Criolla” Colombia variety, 15 from S. tuberosum 
ICA “Puracé” variety, and the remaining 33 from other 
tetraploid regional varieties.
The P. infestans isolates collected in this work were obtained 
from leaflets and petiole portions with symptoms of potato 
blight in potato crops. To purify the strains, symptomatic 
tissues were placed on “Tuquerreña” variety potato slices 
3872010 Silva Aguilar, Cotes, and Marín: Population structure of Phytophthora infestans...
to induce mycelium growth, which was transferred to a rye 
agar medium (25 g rye meal, 18 g of agar, 20 g of sugar, 1 
L distilled water) and kept at 4°C. 
AFLP Tests 
DNA extraction from the isolates was carried out by fol-
lowing the methodology described by Silva et al. (2009). 
For the initial standardization of the AFLPs, five isolates 
were taken from different locations, evaluating 15 primer 
combinations derived from the restriction sites: EcoRI +0 
(5´-GACTGCGTACCAATT-3´) and MseI +0 (5´-GAT-
GAGTCCTGAGTA-3´): EA-MA, EA-MG, EC-MA, EC-
MC, EC-MAC, EC-MCC, EC-MG, EC-MCT, EC-MCG, 
EA-MC, EA-MAC, EA-MCC, EA-MCT, EA-MCG, and 
EAT-MA. Of these combinations, the most polymorphic 
and which were consequently selected for the general 
population analysis corresponded to the primers: EC-MA, 
EC-MCG, EC-MCC, and EC-MCT.
Thereafter, double digestions were performed with the 
EcoRI/MseI enzymes from 5 mL DNA [approx. 100 ng mL-
1], 2X Tango Y Buffer + 1.25 U of the restriction enzymes, 
1 mM of Dithiothreitol (DTT) to fit a total volume of 12.5 
mL. The mixture was incubated at 37°C during 2 h and the 
reactions were halted at 70°C for 15 min. The effectiveness of 
the restriction was monitored in agarose gel at 2% for liga-
tion of Ad-MseI adaptors: 5́ -GACGATGAGTCCTGAG-3́ , 
5´-TACTCAGGACTCAT-3´ and Ad-EcoRI: 5´-CTCG-
TAGACTGCGTACC-3 ,́ 5´-AATTGGTACGCAGTC-
TAC-3́ . The ligation reactions consisted in 25 mL of the final 
volume, including the 12.5 mL of digestion solution, 1 U of 
the T4 DNA ligase enzyme, 5 pmoles/mL of EcoRI adaptor, 
50 pmoles/mL of MseI adaptor, 1 X of enzyme buffer, 0.5 mM 
of DTT, and 0.4 mM of ATP. The mixture was incubated at 
20°C for 2 h and stored at -20°C until its use. To visualize 
the digestion-ligation, 5 mL of the solution were taken and 
electrophoresis was conducted in agarose gel at 1.5%. 
Then, amplifications were carried out via PCR by using the 
sets of primers previously indicated. For the final analysis 
of the AFLP markers, electrophoresis was conducted on 
polyacrylamide gels at 6% + 7.5 M of urea, using a Biorad 
electrophoresis chamber with 25 cm gels. This process 
was begun with a pre-run at 2.300 V and 55°C, to then 
load 5 mL of the previously denatured sample at 95°C for 5 
min and 2 mL of load buffer (100 mL: 0.05 g bromophenol 
blue, 0.05 g xylene cyanol, 10 mL Tris/Borate/EDTA10 X, 
90 mL formamide) and it was run at 2.300 V for 80 min. 
The visualization of the profiles was done by following the 
methodology of silver staining proposed by Sambrook and 
Russell (2001).
Data analysis
For each primer combination a binary matrix was con-
structed based on the presence/absence of each band in the 
isolates evaluated. For the clustering analysis, a matrix of 
distances was obtained based on the Jaccard dissimilarity 
coefficient, and the dendrogram was carried out by using 
the Unweighted Pair Group Method with Arithmetic Mean 
(UPGMA) algorithm, validating the structure of the tree 
based on the value of p (value of p-AU – Approximately 
Unbiased – 0.05 significance level) and probability of oc-
currence obtained through bootstrap, using 10,000 re-
samplings. For this, the pvclust package was used (Susuki 
and Shimodaira, 2006) from the R statistical program (R 
development Core Team, 2006).
Then, the genotype groups were established based on 
their region of origin to conduct a molecular analysis of 
variance (ANOVA) proposed by Excoffier et al. (1992), us-
ing the Arlequin v3.1 software (Institute of Ecology and 
Evolution, University of Bern, Switzerland). A hypothesis 
test was performed for the components of variance among 
and within populations using 1.000 permutations. Finally, 
the number of polymorphic loci was calculated, along with 
the Nei (H) genetic diversity index, the Shannon (I) geno-
typic diversity index, and the population sub-structuring 
statistics: F-statistic (Fst), Nei’s population differentiation 
coefficient (Gst), and the number of average migrants per 
generation (Nm) through the POPGENE software (Uni-
versity of Alberta, Canada).
Results
The initial evaluation of the 15 primer combinations in 
five P. infestans isolates indicated a high level of monomor-
phism, selecting the four combinations resulting slightly 
polymorphic (EC–MA, EC-MCG, EC-MCC, EC-MCT). 
For the construction of the binary matrix, 196 amplicons 
were selected, distributed thus: EC-MA: 55, EC-MCG: 50, 
EC-MCC: 47, and EC-MCT: 44 amplicons. The size of these 
products ranged between 80 and 1.100 bp. In spite of having 
used the methodology in the 160 isolates, the final analysis 
was done based on the 148 isolates amplifying for the four 
pairs of primers (Antioquia: 37, Boyaca: 35, Cundinamarca 
39, and Norte de Santander: 37). 
The genetic analysis of populations generated a value of 
Fst = 0.7 and Gst = 0.42 (P = 0.00001), with the genetic 
distance being greater among the population obtained in 
Antioquia and that from the Cundinamarca and Boyaca 
savannah and Norte de Santander (Tab. 1). The number 
of average migrants per generation was 0.67. When the 
388 Agron. Colomb. 28(3) 2010
TABLE 1. Genetic distance in populations of Phytophthora infestans collected from different varieties Solanum tuberosum and S. phureja in four 
departments of Colombia.
Departments Antioquia Cundinamarca Norte de Santander
Cundinamarca 0.50393
Norte de Santander 0.56964 0.43501
Boyaca 0.49539 0.41023 0.41252
population from Antioquia was not included,the value of 
Nm increased to 0.98 migrants/generation and the degree of 
sub-structuring diminished to 0.34. The populations from 
Boyaca and Cundinamarca presented the least genetic dif-
ferentiation (Gst = 0.26) and the greatest rates of migration 
(Nm = 1.35) (Tab. 2).
The percentage of polymorphic loci ranged between 34 
and 47% (82.65% among the four populations), Nei’s ge-
netic diversity index was between 0.044 and 0.073 (H = 
0.090 for the whole population) and Shannon’s genotypic 
diversity index was between 0.079 and 0.12 (I = 0.158, for 
the whole population) (Tab. 3). ANOVA indicated that the 
total genetic variation of the population under study can be 
explained in 47.2% by differences among the groups, while 
52.8% was due to the variance among the groups.
Based on the dendrogram generated, isolates were separated 
in four groups (I, II, III, and IV) with a maximum distance 
of 0.12, while within each group there was a very high level 
of genetic similarity with values of 0.93, 0.94, 0.92, and 0.91 
for groups I, II, III, and IV, respectively (Fig. 1). The statisti-
cal analysis supporting these groupings resulted high when 
using the P value (group I: 99%, group II: 100%, group III: 
91%, and group IV: 89%), but not for bootstrap values that 
presented a range of 56 to 96% (Fig. 1). The first group (I) 
included 44 isolates that were mostly from the department 
of Antioquia, although five isolates from Boyaca and five 
from Cundinamarca were presented. Group II contained 37 
isolates, 33 from Norte de Santander, and a very low number 
from other regions (one from Cundinamarca, one from Boy-
aca and two from Antioquia); while group III included only 
isolates from Cundinamarca (32) and group IV was made 
up of 29 isolates from Boyaca, one from Cundinamarca, one 
from Antioquia, and four from Norte de Santander.
Discussion
This research presents a genetic study of characteristics of 
P. infestans populations in potato crops in Colombia, which 
included four populations from main potato-growing 
regions in Antioquia, Boyaca, Cundinamarca, and Norte 
de Santander, whose cultivated area corresponds to 77% 
of the total crops with this tuber in the country (122,617 
ha) (MADR, 2006). Our experimental development was 
based on the use of AFLP markers, a methodology that 
is broadly used in these types of studies (Cooke and Lees, 
2004; Gotoh et al., 2005) and, hence, constitutes a strong 
support for the findings in this research. 
Work done by Gilchrist et al. (2009) in 2001; Raigosa et 
al. (2009); Silva et al. (2009) and Vargas et al. (2009) show 
TABLE 2. Analysis of genetic sub-structuring and migration among four populations of P. infestans in Colombia. Values below the diagonal correspond to 
the rate of genetic sub-structuring (Gst = (Ht - Hs)/Ht) values above the diagonal represent the number of migrants/generation (Nm = 0.5 (1 - Gst)/Gst).
Departments Antioquia Boyaca Cundinamarca Norte de Santander
Antioquia 0.91 0.86 0.65
Boyaca 0.35 1.35 1.34
Cundinamarca 0.36 0.26 1.21
Norte de Santander 0.43 0.27 0.29
TABLE 3. Index of diversity found in populations of Phytophthora infestans from Solanum tuberosum and S. phureja in four departments of Colombia.
Index Antioquia Boyaca Cundinamarca Norte de Santander Mean index of all populations
Number of polymorphic loci 93 93 92 68 128
Proportion of polymorphic loci 47.40 47.40 46.90 34.60 82.65
Nei (H) genetic diversity index 0.045±0.0237 0.073±0.037 0.056±0.029 0.044±0.022 0.090±0.135
Shannon (I) genotypic diversity 
index
0.085±0.103 0.120±0.1686 0.100±0.141 0.079±0.1345 0.158±0.194
3892010 Silva Aguilar, Cotes, and Marín: Population structure of Phytophthora infestans...
FIgURE 1. Dendrogram generated by UPGMA analysis of AFLP markers for a population of 148 isolates of P. infestans collected from four 
departments of Colombia. Numbers on branches indicate the value P (above) and bootstrap probability (below). Roman numerals indicate the 
population and are explained in the text.
390 Agron. Colomb. 28(3) 2010
the occurrence of only one type mating and of one mito-
chondrial haplotype predominant in the potato P. infestans 
populations; nevertheless, Vargas et al. (2009) reported in 
Colombia the presence of an isolate with the A2 type from P. 
peruviana plants. The genetic variability analysis performed 
via AFLP markers revealed variation among and within the 
four populations evaluated. Although said variation levels 
were low (H = 0.090; I = 0.158), all the isolates evaluated 
correspond to unique genotypes, which in many cases only 
diverge by a few loci. These variation levels indirectly indicate 
the absence of sexual reproduction of this pathogen in Co-
lombia, and support the hypothesis that other mechanisms 
like parasexuality, high rates of mutations, and presence 
of extra-chromosomal elements are important in defining 
P. infestans populations. These mechanisms have already 
been experimentally detected when evaluating the geno-
types derived from monozoosporic crops through RAPD 
and AFLP molecular markers (Abu-El Samen et al., 2003). 
These authors found a considerable level of molecular and 
phenotypic variation in the monozoosporic populations 
evaluated, suggesting that genetic changes in asexual P. 
infestans populations are possible and that these affect the 
resulting phenotypes, both at the level of pathogenicity, as 
well as of sensitivity to some fungicides. This situation was 
confirmed by Gilchrist et al., (2009) in a population of 28 
P. infestans isolates from potato crops in Antioquia, which 
represented 18 pathotypes different from the oomycete and 
contained in all 10 of the 11 factors of virulence identified in 
the world to define the P. infestans-S. tuberosum interaction.
The studies conducted with molecular markers like AFLPs 
and microsatellites in P. infestans populations have per-
mitted inferring with greater precision the levels of vari-
ability presented by this pathogen and that through the 
conventional methods defining the genetic lineages (RFLP 
with the RG57 probe, analysis of Gpi and Pep isoenzymes, 
mating type, resistance to metalaxyl and mitochondrial 
haplotypes) were generally masked (Cooke and Lees, 2004). 
Thus, for example, Cooke et al. (2003) evaluated the P. 
infestans populations in Scotland between 1995 and 1997, 
and found that from a sample of 500 isolates, there were 
only two mitochondrial haplotypes (Ia and IIa) and six 
RG57 electrophoretic profiles, while the AFLP analysis 
detected high levels of variability (H= 0.39; I= 0.57) and the 
presence of at least half of the population evaluated with 
unique AFLP patterns. Similarly, Knapova and Gisi (2002), 
when studying P. infestans populations collected between 
1996 and 1997 in France and Switzerland, found that for 
every nine isolates analyzed with microsatellites, one cor-
responded to a different genotype and that said proportion 
was two to one, when using AFLP markers.
In the Andean region, two studies have been published on 
P. infestans populations using AFLP markers. The first of 
these, corresponds to that conducted by Adler et al. (2004) 
with a population of the pathogen from different hosts (S. 
andreanum, S. colombianum, S. caripense, S. muricatum, 
S. tuberosum, S. betaceum, Brugmansia sanguinea, among 
others) and which permitted the separation of the popula-
tion into several clades representing the EC-1, US-1, EC-3 
lineages, besides the Ic and Ia haplotypes, associated to 
new lineages in S. muricatum and in Solanum species from 
the Anarrhichomenum section, respectively. Within each 
group several sub-clades were presented, revealed variation 
among the isolates that comprise them. The main clades 
presented considerable genetic distances that even led 
to the description of the new P. andina species from the 
isolates obtained in S. tetrapetalum of Anarrhichomenum 
(Adler et al., 2004; Gómez et al., 2007). The other study 
was conducted by Mesa et al. (2008) withtwo P. infestans 
populations collected in the department of Nariño and 
obtained in potato and tree tomato crops. In said work, 
the populations from both hosts were located in different 
clades and presented genetic differentiation (Fst= 0.12; P 
= 0.0001). Additionally, a certain level of genetic variation 
was found within each group (H= 0.04; I= 0.06). Such a 
variation was similar to that found within each of the P. 
infestans populations from the four departments included 
in this study (H= 0.04 to 0.07), which may indicate that 
in spite of the differences in each of the study zones, the 
pathogen in Colombia presents some similar population 
parameters, with the absence of sexual reproduction in the 
populations being a determining factor for this situation.
On the other hand, in this study, the analysis of the popula-
tion structure from the AFLP markers permitted determin-
ing the existence of genetic differentiation among the four 
populations, especially among the P. infestans population 
from Antioquia and those from the middle-east part of the 
country, which present a lower degree of sub-structuring 
(Gst < 0.3), probably as a result of a greater genetic flow of 
its populations (Nm > 1.21). Said situation can be due to 
the differences existing in the environmental conditions 
in both regions, especially those related with rainfall and 
temperature, besides the important selection effect rep-
resented by the cultivation of different varieties and the 
differences in the management practices by farmers in said 
zones. In Antioquia predominates the cultivation of the 
“Diacol Capiro” variety, while in Boyaca, Cundinamarca, 
and Norte de Santander the “Parda Pastusa” variety is 
cultivated most, although there is increased cultivation of 
improved material resistant to P. infestans, like “Pastusa 
Suprema” (Santos et al., 2010).
3912010 Silva Aguilar, Cotes, and Marín: Population structure of Phytophthora infestans...
The other mechanism that could explain the sub-structuring 
found corresponds to the geographical isolation between 
the two areas. Nevertheless, when considering the flow of 
seed tuber between these regions and of fresh commercial-
ized potato, this hypothesis loses value and on the contrary 
reaffirms the importance in both regions of selection factors 
of genotypes of the pathogen like climate and agronomic 
management, more so when the grouping of some isolates 
was detected in representative clades from different places 
to their place of origin. These isolates can be considered part 
of founder populations, which are in the process of adapting 
to the new conditions of the agro-ecosystems and represent 
a possible risk, given that they introduce new sets of genes to 
these zones, which can derive into variants that are more path-
ogenic or resistant to fungicides used to control potato blight.
The greatest variability within the P. infestans popula-
tion in Antioquia and its difference with the rest of the 
populations, indicate that the varieties improved through 
resistance to potato blight must be evaluated in the potato-
growing zones of this department, which coincides with 
field observations made by Henfling (1987), when making 
evaluations in the Corpoica research station “La Selva” in 
Rionegro, with some families from crosses showing resis-
tance to P. infestans.
Conclusions
The characteristics of the P. infestans population structure 
in four potato-growing departments in Colombia are pre-
sented in this study. The validity of their results is supported 
by the high number of isolates evaluated (148) and by the 
use of AFLP molecular markers, which revealed a low level 
of variation within the geographical populations evaluated. 
The sub-structuring analysis showed differentiation among 
the P. infestans population from Antioquia and those ob-
tained from the departments of Boyaca, Cundinamarca, 
and Norte de Santander. 
The results suggest that the occurrence of parasexual 
phenomena or high rates of mutation in this pathogen are 
important in the definition of the population characteris-
tics of P. infestans in Colombia and that it is necessary to 
include the evaluation of the improved potato materials in 
the cultivation regions of Antioquia, given the differences 
of the pathogen populations in this department.
Acknowledgments
This research was funded by the Research Office at Univer-
sidad Nacional de Colombia (project: 20101005571) and by 
DIME (Laboratory Enhancement Project, Medellin). The 
collection of isolates used in the study was carried out with 
the support from technical personnel from Fedepapa and 
from Professor Sonia Jaramillo and farmers in Antioquia, 
Boyaca, Cundinamarca, and Norte de Santander.
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